Monthly Archives: December 2013

Post navigation

I love this science video. Creative and innovative. Great job ladies and gents. We need more of these to show that science really is fun.

Oh, and I want one of those hats for the next conference!!! How cool is that!

Enjoy, smile and Happy New Year to everyone!

The lyrics are shown below the video on YouTube, but here they are as well:

Hello? Hello? Baby, you called. I can’t hear a thing.
I have got not service in the laboratory.
I have got no time for talking. Baby, can’t you see?
I am trying to study some biochemistry.

When the chromosomes condense then we call it prophase.
And when they line up then it is called metaphase.
When they pull apart then we call it anaphase.
And when they divide into two cells that is telophase.

Stop calling. Stop calling. I don’t wanna talk anymore.
I have a test that I am studying for.

GTACCCGTAGT
Neucleotides are
CATGGGATCA
They go
TACATGTCT
Neucleotides are
ACTTCGGAATA

DNA wrapped around histones.
It’s all in the chromosome.
Everything in your genome:
It’s all in the chromosome.

And when those cells explode they call it apoptosis.
Different than necrosis. Not caused by osmosis.
It’s dangerous when the cell begin undergoing anoikis.
Then there’s metastasis. Cell death is so tasteless.

DNA is simple if at first you only think,
That you have a purine paired with a pyrimidine.
The sugar-phosphate backbone holds all the bases
Which is twisted around like a spiral staircase.

Copying, copying like in vivo but much faster.
I got my genes from the lab thermocycler.

Like this:

People are beginning to ask about how they can obtain some of the health information that they were previously receiving from 23andMe. For $5, at Promethease, you can upload any of the autosomal files from either Family Tree DNA, 23andMe or Ancestry.com. They will process your raw data and provide you with a report that is available to download from their server for 45 days. They also e-mail you a copy.

At Promethease, your raw data file is deleted within 24 hours of completion of your report, and your report file will be deleted after 45 days, so be sure to download your report for future reference. Currently they process about 20,000 genotypes, or SNPs. They do note that they update their data base regularly from SNPedia, fed from PubMed publications. Therefore your report in the future will include SNPs that won’t be in your report today and what we’ve learned about those SNPs may differ as well.

They have also noted that you receive different items in your report based on which vendor’s full data file you submit. That’s true. I uploaded all 3 of my raw data files, from Ancestry, 23andMe and Family Tree DNA and ran Promethease against each of them. While 23andMe optimized their chip for medical and health results, Family Tree DNA intentionally removed some medically relevant data in order to avoid any FDA type of issues. It’s unknown how Ancestry treats medically significant SNPs, but I’m running all 3 vendor’s files to view differences.

You will then be asked to select an ethnicity. I always hate this question, because I’m more than one and the categories never fit. If you don’t fit any category well, select the closest. Promethease says it only affects the sort order. That was a relief to me, as I always wonder what I’m missing by making one selection over another.

While the report actually runs, which takes about 15-20 minutes, amuse yourself by watching the video about how to download, read and understand your results. Or you could write a blog, like me!

You can review this video at any time by visiting the original link. It does make more sense after you have your report in hand.

My report only took 8 minutes to run, and according to the front page of my report, they analyzed over 20,000 SNPs or known mutation locations. I’m excited to see what my report holds.

One of the reasons I’ve been interested in this type of DNA reporting is that my mother was “diagnosed” with Parkinson’s Disease. I put diagnosed in quotes, because Parkinson’s is a diagnosis of exclusion, for which there is no specific diagnostic test, meaning the diagnosis is one made after other alternative diseases for which there are tests, are excluded. However, she never had some of the traditional symptoms, like the specific walking gait typical in Parkinson’s patients, nor some of the other symptoms, nor were the Parkinson’s medications effective in controlling her hand tremors. Her father also had the same tremors, which I’ve always suspected was Familial Tremor, not Parkinson’s. I wanted to see if Mom or I carried elevated risk for Parkinson’s. Mom’s DNA was archived at Family Tree DNA, so I could run the Family Finder test even though she had passed away by the time autosomal testing was available. So I uploaded and ran her file at Promethease too, and compared with my own.

So, let’s look at my report based on the 23andMe raw data file.

At this point, you have to choose to click on “Bad News” or “Good News” first. Someone should do a study about whether you select bad or good is genetically influenced.

In my case, I was interested to see if my “bad news” was the same “bad news” that 23andMe provided. My top “bad news” item is indeed the same item that is reported at 23andMe. Having said that, there are a lot more and different items here that were not reported at 23andMe. After looking at the varied results from Promethease, I suspect that 23andMe was trying to distill data on my behalf.

However, Promethease does not attempt to analyze your results. Some mutations are known to be connected to multiple conditions, so they simply tell you that. In some cases, you will have some negative and some positive mutations for the same disease. Again, they simply inform you, complete with a reference. It’s worth noting that for one disease I’m particularly interested in, Parkinson’s, I have a lot of conflicting data, pages worth. This just goes to show how complex interpreting this information really is, and shows that genetic predisposition, positive or negative, with only a few exceptions, is not genetic predetermination.

My good news made me feel really good. I’m at decreased risk of frontotemporal dementia or Alzheimer’s and Parkinson’s. I’m optimistic and empathetic. I wonder if this has anything to do with selecting the bad news option first – I knew I had the good news to look forward to. Get the bad stuff over with and get on with it…

Ironically, some of my good news items are in direct conflict with some of my bad news items. And yes, some are Parkinson’s, which has apparently been more heavily studied that some other diseases. Hopefully, the decreased and elevated risks will cancel each other out and I’ll just be average.

However, when running my Ancestry data file at Promethease, one of my elevated risks was Parkinson’s, based on the SNPs discovered in the 23andMe research, which conflicts directly with the information provided based on the 23andMe raw data file. Searching further, different SNPs have been reported to either be associated with increased or decreased incidence of the disease – and I carry some of each – but none are extremely elevated.

So where does this leave me in terms of whether Mom had Parkinson’s, or not? There is nothing to indicate an extremely high risk of Parkinson’s. Some indicators are for elevated risk, some for reduced risk. Compared to the one condition I know she had, which has a very highly elevated risk in all 3 reports, the Parkinson’s risk is simply unremarkable and doesn’t stand out. Bottom line – I still don’t know for sure, but I still don’t think she had Parkinson’s. Had I found highly elevated risk factors, I would have rethought my opinion.

Many diseases have multiple genetic components along with other external factors. Of course, not all studies report the same findings, and this report is based on academic medical studies.

Rarely are genetic predispositions more than just that, a slightly increased or decreased probability. Few are fatal and some are more of a life sentence than a death sentence. Having said this, there are notable exceptions, and if you really don’t want to know a worst case scenario, or aren’t prepared to deal with the results, don’t participate in DNA testing or reporting for medical or health information. If you have reason to suspect your family may carry one of the genetic terminal illnesses, visit your doctor for advice.

And speaking of physicians, much of this information, such as the information about how certain medications are metabolized could be critically important. In my case, I’m actually taking one of the mediations that is referenced where I have a decreased sensitivity. Yep, I knew that, but now I can provide this information to my physician.

For those who tend to worry and borrow trouble they don’t yet have, running this type of report might not be a good idea. It’s certainly not for hypochondriacs – IMHO. It’s a personal choice, and a very inexpensive one at that, so financially available to everyone. If what it contains is going to worry you, don’t do it. I noticed that there are several anxiety categories in these reports – but then you have to run the report to see if you carry them – kind of a catch 22 if you tend to be anxious and worry.

My personal perspective is that there may be information here that is valuable to me, or to my physicians, or to my children. The worst “bad news” item I already knew about through 23andMe, but I also anticipated that condition, without genetic testing, because my mother had this same disease in old age. I’m not referring now to the Parkinson’s, but a vision related condition that she definitely did have. This item was also consistently reported at a high degree of risk utilizing the data files of 23andMe, Family Tree DNA and Ancestry. Thankfully, it is an old age problem and one that can be treated, if not cured today. The Promethease reports, along with 23andMe’s report, have simply reinforced that I need to be proactive and vigilant and to eat lots of veggies. The good news is that many items include preventative measures in the verbiage or associated studies that your Promethease report links to at SNPedia.

How does this report compare to the 23andMe experience, assuming 23andMe was still an option or might be again in the future for health information? The 23andMe customer interface is much smoother and more user friendly. It seems to be focused on more “fun” and less “worry.” The Promethease report is that, a report, although they do a great job making it interactive. There is no sugar coating – just the facts Ma’am. And I think it’s actually much easier to use. You can easily search by disease, by category, and the searches actually work.

Promethease differs in another way too. Personally I like the idea that my data is mine, I’m in complete control of it, and it’s not being sold by Promethease out the back door for studies or purposes I might not be too thrilled about. I don’t want my DNA to be used to patent genes that cause the tests for the condition to be restricted to the patentee at dramatically inflated prices. While the Supreme Court determined that genes can’t be patented in the case of the BRCA breast cancer genes, the fight continues with lawsuits being filed, and 23andMe holds a Parkinson’s patent that was obtained by utilizing customer data. Nor do I want my data to be used to patent the technology for “designer babies.” If my DNA is going to be utilized for research, I want the ability to authorize that use, specifically.

Therefore, I feel much better about uploading a raw data file from an autosomal test at a firm like Family Tree DNA, who NEVER sells or otherwise divulges my data without first requesting permission. I thereby maintain complete control over my genetic results, rather than utilizing companies who either sell (or otherwise utilize) my results or reserve the right to do so. This is the case with both 23andMe and Ancestry.com, and to be clear, they have never claimed otherwise.

And oh, I forgot to mention…I am just so relieved….I have a decreased risk of baldness….

Last year I wrote a column at the end of the year titled “2012 Top 10 Genetic Genealogy Happenings.” It’s amazing the changes in this industry in just one year. It certainly makes me wonder what the landscape a year from now will look like.

I’ve done the same thing this year, except we have a dozen. I couldn’t whittle it down to 10, partly because there has been so much more going on and so much change – or in the case of Ancestry, who is noteworthy because they had so little positive movement.

If I were to characterize this year of genetic genealogy, I would call it The Year of the SNP, because that applies to both Y DNA and autosomal. Maybe I’d call it The Legal SNP, because it is also the year of law, court decisions, lawsuits and FDA intervention. To say it has been interesting is like calling the Eiffel Tower an oversized coat hanger.

I’ll say one thing…it has kept those of us who work and play in this industry hopping busy! I guarantee you, the words “I’m bored” have come out of the mouth of no one in this industry this past year.

I’ve put these events in what I consider to be relatively accurate order. We could debate all day about whether the SNP Tsunami or the 23andMe mess is more important or relevant – and there would be lots of arguing points and counterpoints…see…I told you lawyers were involved….but in reality, we don’t know yet, and in the end….it doesn’t matter what order they are in on the list:)

Y Chromosome SNP Tsunami Begins

The SNP tsumani began as a ripple a few years ago with the introduction at Family Tree DNA of the Walk the Y program in 2007. This was an intensively manual process of SNP discovery, but it was effective.

By the time that the Geno 2.0 chip was introduced in 2012, 12,000+ SNPs would be included on that chip, including many that were always presumed to be equivalent and not regularly tested. However, the Nat Geo chip tested them and indeed, the Y tree became massively shuffled. The resolution to this tree shuffling hasn’t yet come out in the wash. Family Tree DNA can’t really update their Y tree until a publication comes out with the new tree defined. That publication has been discussed and anticipated for some time now, but it has yet to materialize. In the mean time, the volunteers who maintain the ISOGG tree are swamped, to say the least.

Another similar test is the Chromo2 introduced this year by Britain’s DNA which scans 15,000 SNPs, many of them S SNPs not on the tree nor academically published, adding to the difficulty of figuring out where they fit on the Y tree. While there are some very happy campers with their Chromo2 results, there is also a great deal of sloppy science, reporting and interpretation of “facts” through this company. Kind of like Jekyll and Hyde. See the Sloppy Science section.

But Walk the Y, Chromo2 and Geno 2.0, are only the tip of the iceburg. The new “full Y” sequencing tests brought into the marketspace quietly in early 2013 by Full Genomes and then with a bang by Family Tree DNA with the their Big Y in November promise to revolutionize what we know about the Y chromosome by discovering thousands of previously unknown SNPs. This will in effect swamp the Y tree whose branches we thought were already pretty robust, with thousands and thousands of leaves.

In essence, the promise of the “fully” sequenced Y is that what we might term personal or family SNPs will make SNP testing as useful as STR testing and give us yet another genealogy tool with which to separate various lines of one genetic family and to ratchet down on the time that the most common recent ancestor lived.

The story of 23andMe began as the consummate American dotcom fairy tale, but sadly, has deteriorated into a saga with all of the components of a soap opera. A wealthy wife starts what could be viewed as an upscale hobby business, followed by a messy divorce and a mystery run-in with the powerful overlording evil-step-mother FDA. One of the founders of 23andMe is/was married to the founder of Google, so funding, at least initially wasn’t an issue, giving 23andMe the opportunity to make an unprecedented contribution in the genetic, health care and genetic genealogy world.

Another way of looking at this is that 23andMe is the epitome of the American Dream business, a startup, with altruism and good health, both thrown in for good measure, well intentioned, but poorly managed. And as customers, be it for health or genealogy or both, we all bought into the altruistic “feel good” culture of helping find cures for dread diseases, like Parkinson’s, Alzheimer’s and cancer by contributing our DNA and responding to surveys.

The genetic genealogy community’s love affair with 23andMe began in 2009 when 23andMe started focusing on genealogy reporting for their tests, meaning cousin matches. We, as a community, suddenly woke up and started ordering these tests in droves. A few months later, Family Tree DNA also began offering this type of testing as well. The defining difference being that 23andMe’s primary focus has always been on health and medical information with Family Tree DNA focused on genetic genealogy. To 23andMe, the genetic genealogy community was an afterthought and genetic genealogy was just another marketing avenue to obtain more people for their health research data base. For us, that wasn’t necessarily a bad thing.

For awhile, this love affair went along swimmingly, but then, in 2012, 23andMe obtained a patent for Parkinson’s Disease. That act caused a lot of people to begin to question the corporate focus of 23andMe in the larger quagmire of the ethics of patenting genes as a whole. Judy Russell, the Legal Genealogist, discussed this here. It’s difficult to defend 23andMe’s Parkinson’s patent while flaying alive Myriad for their BRCA patent. Was 23andMe really as altruistic as they would have us believe?

Personally, this event made me very nervous, but I withheld judgment. But clearly, that was not the purpose for which I thought my DNA, and others, was being used.

But then came the Designer Baby patent in 2013. This made me decidedly uncomfortable. Yes, I know, some people said this really can’t be done, today, while others said that it’s being done anyway in some aspects…but the fact that this has been the corporate focus of 23andMe with their research, using our data, bothered me a great deal. I have absolutely no issue with using this information to assure or select for healthy offspring – but I have a personal issue with technology to enable parents who would select a “beauty child,” one with blonde hair and blue eyes and who has the correct muscles to be a star athlete, or cheerleader, or whatever their vision of their as-yet-unconceived “perfect” child would be. And clearly, based on 23andMe’s own patent submission, that is the focus of their patent.

Upon the issuance of the patent, 23andMe then said they have no intention of using it. They did not say they won’t sell it. This also makes absolutely no business sense, to focus valuable corporate resources on something you have no intention of using? So either they weren’t being truthful, they lack effective management or they’ve changed their mind, but didn’t state such.

What came next, in late 2013 certainly points towards a lack of responsible management.

23andMe had been working with the FDA for approval the health and medical aspect of their product (which they were already providing to consumers prior to the November 22nd cease and desist order) for several years. The FDA wants assurances that what 23andMe is telling consumers is accurate. Based on the letter issued to 23andMe on November 22nd, and subsequent commentary, it appears that both entities were jointly working towards that common goal…until earlier this year when 23andMe mysteriously “somehow forgot” about the FDA, the information they owed them, their submissions, etc. They also forgot their phone number and their e-mail addresses apparently as well, because the FDA said they had heard nothing from them in 6 months, which backdates to May of 2013.

It may be relevant that 23andMe added the executive position of President and filled it in June of 2013, and there was a lot of corporate housecleaning that went on at that time. However, regardless of who got housecleaned, the responsibility for working with the FDA falls squarely on the shoulders of the founders, owners and executives of the company. Period. No excuses. Something that critically important should be on the agenda of every executive management meeting. Why? In terms of corporate risk, this was obviously a very high risk item, perhaps the highest risk item, because the FDA can literally shut their doors and destroy them. There is little they can do to control or affect the FDA situation, except to work with the FDA, meet deadlines and engender goodwill and a spirit of cooperation. The risk of not doing that is exactly what happened.

It’s unknown at this time if 23andMe is really that corporately arrogant to think they could simply ignore the FDA, or blatantly corporately negligent or maybe simply corporately stupid, but they surely betrayed the trust and confidence of their customers by failing to meet their commitments with and to the FDA, or even communicate with them. I mean, really, what were they thinking?

There has been an outpouring of sympathy for 23andme and negative backlash towards the FDA for their letter forcing 23andMe to stop selling their offending medical product, meaning the health portion of their testing. However, in reality, the FDA was only meting out the consequences that 23andMe asked for. My teenage kids knew this would happen. If you do what you’re not supposed to….X, Y and Z will, or won’t, happen. It’s called accountability. Just ask my son about his prom….he remembers vividly. Now why my kids, or 23andMe, would push an authority figure to that point, knowing full well the consequences, utterly mystifies me. It did when my son was a teenager and it does with 23andMe as well.

Some people think that the FDA is trying to stand between consumers and their health information. I don’t think so, at least not in this case. Why I think that is because the FDA left the raw data files alone and they left the genetic genealogy aspect alone. The FDA knows full well you can download your raw data and for $5 process it at a third party site, obtaining health related genetic information. The difference is that Promethease is not interpreting any data for you, only providing information.

There is some good news in this and that is that from a genetic genealogy perspective, we seem to be safe, at least for now, from government interference with the testing that has been so productive for genetic genealogy. The FDA had the perfect opportunity to squish us like a bug (thanks to the opening provided by 23andMe,) and they didn’t.

The really frustrating aspect of this is that 23andMe was a company who, with their deep pockets in Silicon Valley and other investors, could actually afford to wage a fight with the FDA, if need be. The other companies who received the original 2010 FDA letter all went elsewhere and focused on something else. But 23andMe didn’t, they decided to fight the fight, and we all supported their decision. But they let us all down. The fight they are fighting now is not the battle we anticipated, but one brought upon themselves by their own negligence. This battle didn’t have to happen, and it may impair them financially to such a degree that if they need to fight the big fight, they won’t be able to.

Right now, 23andMe is selling their kits, but only as an ancestry product as they work through whatever process they are working through with the FDA. Unfortunately, 23andMe is currently having some difficulties where the majority of matches are disappearing from some testers records. In other cases, segments that previously matched are disappearing. One would think, with their only revenue stream for now being the genetic genealogy marketspace that they would be wearing kid gloves and being extremely careful, but apparently not. They might even consider making some of the changes and enhancements we’ve requested for so long that have fallen on deaf ears.

One thing is for sure, it will be extremely interesting to see where 23andMe is this time next year. The soap opera continues.

I hope for the sake of all of the health consumers, both current and (potentially) future, that this dotcom fairy tale has a happy ending.

In a landmark decision, the Supreme Court determined that genes cannot be patented. Myriad Genetics held patents on two BRCA genes that predisposed people to cancer. The cost for the tests through Myriad was about $3000. Six hours after the Supreme Court decision, Gene By Gene announced that same test for $995. Other firms followed suit, and all were subsequently sued by Myriad for patent infringement. I was shocked by this, but as one of my lawyer friends clearly pointed out, you can sue anyone for anything. Making it stick is yet another matter. Many firms settle to avoid long and very expensive legal battles. Clearly, this issue is not yet resolved, although one would think a Supreme Court decision would be pretty definitive. It potentially won’t be settled for a long time.

As 23andMe comes unraveled and Ancestry languishes in its mediocrity, Gene by Gene, the parent company of Family Tree DNA has stepped up to the plate, committed to do “whatever it takes,” ramped up the staff both through hiring and acquisitions, and is producing results. This is, indeed, a breath of fresh air for genetic genealogists, as well as a welcome relief.

Autosomal DNA testing and analysis has simply exploded this past year. More and more people are testing, in part, because Ancestry.com has a captive audience in their subscription data base and more than a quarter million of those subscribers have purchased autosomal DNA tests. That’s a good thing, in general, but there are some negative aspects relative to Ancestry, which are in the Ancestry section.

Another boon to autosomal testing was the 23andMe push to obtain a million records. Of course, the operative word here is “was” but that may revive when the FDA issue is resolved. One of the down sides to the 23andMe data base, aside from the fact that it’s not genealogist friendly, is that so many people, about 90%, don’t communicate. They aren’t interested in genealogy.

A third factor is that Family Tree DNA has provided transfer ability for files from both 23andMe and Ancestry into their data base.

Fourth is the site, GedMatch, at www.gedmatch.com which provides additional matching and admixture tools and the ability to match below thresholds set by the testing companies. This is sometimes critically important, especially when comparing to known cousins who just don’t happen to match at the higher thresholds, for example. Unfortunately, not enough people know about GedMatch, or are willing to download their files. Also unfortunate is that GedMatch has struggled for the past few months to keep up with the demand placed on their site and resources.

A great deal of time this year has been spent by those of us in the education aspect of genetic genealogy, in whatever our capacity, teaching about how to utilize autosomal results. It’s not necessarily straightforward. For example, I wrote a 9 part series titled “The Autosomal Me” which detailed how to utilize chromosome mapping for finding minority ethnic admixture, which was, in my case, both Native and African American.

As the year ends, we have Family Tree DNA, 23andMe and Ancestry who offer the autosomal test which includes the relative-matching aspect. Fortunately, we also have third party tools like www.GedMatch.com and www.DNAGedcom.com, without which we would be significantly hamstrung. In the case of DNAGedcom, we would be unable to perform chromosome segment matching and triangulation with 23andMe data without Rob Warthen’s invaluable tool.

While this tool, www.dnagedcom.com, falls into the Autosomal grouping, I have separated it out for individual mention because without this tool, the progress made this year in autosomal DNA ancestor and chromosomal mapping would have been impossible. Family Tree DNA has always provided segment matching boundaries through their chromosome browser tool, but until recently, you could only download 5 matches at a time. This is no longer the case, but for most of the year, Rob’s tool saved us massive amounts of time.

23andMe does not provide those chromosome boundaries, but utilizing Rob’s tool, you can obtain each of your matches in one download, and then you can obtain the list of who your matches match that is also on your match list by requesting each of those files separately. Multiple steps? Yes, but it’s the only way to obtain this information, and chromosome mapping without the segment data is impossible

A special hats off to Rob. Please remember that Rob’s site is free, meaning it’s donation based. So, please donate if you use the tool.

I covered www.Gedmatch.com in the “Best of 2012” list, but they have struggled this year, beginning when Ancestry announced that raw data file downloads were available. GedMatch consists of two individuals, volunteers, who are still struggling to keep up with the required processing and the tools. They too are donation based, so don’t forget about them if you utilize their tools.

Ancestry – How Great Thou Aren’t

Ancestry is only on this list because of what they haven’t done. When they initially introduced their autosomal product, they didn’t have any search capability, they didn’t have a chromosome browser and they didn’t have raw data file download capability, all of which their competitors had upon first release. All they did have was a list of your matches, with their trees listed, with shakey leaves if you shared a common ancestor on your tree. The implication, was, and is, of course, that if you have a DNA match and a shakey leaf, that IS your link, your genetic link, to each other. Unfortunately, that is NOT the case, as CeCe Moore documented in her blog from Rootstech (starting just below the pictures) as an illustration of WHY we so desperately need a chromosome browser tool.

In a nutshell, Ancestry showed the wrong shakey leaf as the DNA connection – as proven by the fact that both of CeCe’s parents have tested at Ancestry and the shakey leaf person doesn’t match the requisite parent. And there wasn’t just one, not two, but three instances of this. What this means is, of course, that the DNA match and the shakey leaf match are entirely independent of each other. In fact, you could have several common ancestors, but the DNA at any particular location comes only from one on either Mom or Dad’s side – any maybe not even the shakey leaf person.

So what Ancestry customers are receiving is a list of people they match and possible links, but most of them have no idea that this is the case, and blissfully believe they have found their genetic connection. They have found a genealogical cousin, and it MIGHT be the genetic connection. But then again, they could have found that cousin simply by searching for the same ancestor in Ancestry’s data base. No DNA needed.

Ancestry has added a search feature, allowed raw data file downloads (thank you) and they have updated their ethnicity predictions. The ethnicity predictions are certainly different, dramatically different, but equally as unrealistic. See the Ethnicity Makeovers section for more on this. The search function helps, but what we really need is the chromosome browser, which they have steadfastly avoided promising. Instead, they have said that they will give us “something better,” but nothing has materialized.

I want to take this opportunity, to say, as loudly as possible, that TRUST ME IS NOT ACCEPTABLE in any way, shape or form when it comes to genetic matching. I’m not sure what Ancestry has in mind by the way of “better,” but it if it’s anything like the mediocrity with which their existing DNA products have been rolled out, neither I nor any other serious genetic genealogist will be interested, satisfied or placated.

Regardless, it’s been nearly 2 years now. Ancestry has the funds to do development. They are not a small company. This is obviously not a priority because they don’t need to develop this feature. Why is this? Because they can continue to sell tests and to give shakey leaves to customers, most of whom don’t understand the subtle “untruth” inherent in that leaf match – so are quite blissfully happy.

In years past, I worked in the computer industry when IBM was the Big Dog against whom everyone else competed. I’m reminded of an old joke. The IBM sales rep got married, and on his wedding night, he sat on the edge of the bed all night long regaling his bride in glorious detail with stories about just how good it was going to be….

You can sign a petition asking Ancestry to provide a chromosome browser here, and you can submit your request directly to Ancestry as well, although to date, this has not been effective.

The most frustrating aspect of this situation is that Ancestry, with their plethora of trees, savvy marketing and captive audience testers really was positioned to “do it right,” and hasn’t, at least not yet. They seem to be more interested in selling kits and providing shakey leaves that are misleading in terms of what they mean than providing true tools. One wonders if they are afraid that their customers will be “less happy” when they discover the truth and not developing a chromosome browser is a way to keep their customers blissfully in the dark.

This has been a huge year for advances in sequencing ancient DNA, something once thought unachievable. We have learned a great deal, and there are many more skeletal remains just begging to be sequenced. One absolutely fascinating find is that all people not African (and some who are African through backmigration) carry Neanderthal and Denisovan DNA. Just this week, evidence of yet another archaic hominid line has been found in Neanderthal DNA and on Christmas Day, yet another article stating that type 2 Diabetes found in Native Americans has roots in their Neanderthal ancestors. Wow!

Closer to home, by several thousand years is the suggestion that haplogroup R did not exist in Europe after the ice age, and only later, replaced most of the population which, for males, appears to have been primarily haplogroup G. It will be very interesting as the data bases of fully sequenced skeletons are built and compared. The history of our ancestors is held in those precious bones.

Unfortunately, as DNA becomes more mainstream, it becomes a target for both sloppy science or intentional misinterpretation, and possibly both. Unfortunately, without academic publication, we can’t see results or have the sense of security that comes from the peer review process, so we don’t know if the science and conclusions stand up to muster.

The race to the buck in some instances is the catalyst for this. In other cases, and not in the links below, some people intentionally skew interpretations and results in order to either fulfill their own belief agenda or to sell “products and services” that invariably report specific findings.

It’s equally as unfortunate that much of these misconstrued and sensationalized results are coming from a testing company that goes by the names of BritainsDNA, ScotlandsDNA, IrelandsDNA and YorkshiresDNA. It certainly does nothing for their credibility in the eyes of people who are familiar with the topics at hand, but it does garner a lot of press and probably sells a lot of kits to the unwary.

I hope they publish their findings so we can remove the “sloppy science” aspect of this. Sensationalist reporting, while irritating, can be dealt with if the science is sound. However, until the results are published in a peer-reviewed academic journal, we have no way of knowing.

Thankfully, Debbie Kennett has been keeping her thumb on this situation, occurring primarily in the British Isles.

Citizen science has been slowing coming of age over the past few years. By this, I mean when citizen scientists work as part of a team on a significant discovery or paper. Bill Hurst comes to mind with his work with Dr. Doron Behar on his paper, A Copernican Reassessment of the Human Mitochondrial DNA from its Root or what know as the RSRS model. As the years have progressed, more and more discoveries have been made or assisted by citizen scientists, sometimes through our projects and other times through individual research. JOGG, the Journal of Genetic Genealogy, which is currently on hiatus waiting for Dr. Turi King, the new editor, to become available, was a great avenue for peer reviewed publication. Recently, research projects have been set up by citizen scientists, sometimes crowd-funded, for specific areas of research. This is a very new aspect to scientific research, and one not before utilized.

The first paper below includes the Family Tree DNA Lab, Thomas and Astrid Krahn, then with Family Tree DNA and Bonnie Schrack, genetic genealogist and citizen scientist, along with Dr. Michael Hammer from the University of Arizona and others.

Unfortunately, ethnicity percentages, as provided by the major testing companies still disappoint more than thrill, at least for those who have either tested at more than one lab or who pretty well know their ethnicity via an extensive pedigree chart.

Ancestry.com is by far the worse example, swinging like a pendulum from one extreme to the other. But I have to hand it to them, their marketing is amazing. When I signed in, about to discover that my results had literally almost reversed, I was greeted with the banner “a new you.” Yea, a new me, based on Ancestry’s erroneous interpretation. And by reversed, I’m serious. I went from 80% British Isles to 6% and then from 0% Western Europe to 79%. So now, I have an old wrong one and a new wrong one – and indeed they are very different. Of course, neither one is correct…..but those are just pesky details…

23andMe updated their ethnicity product this year as well, and fine tuned it yet another time. My results at 23andMe are relatively accurate. I saw very little change, but others saw more. Some were pleased, some not.

The bottom line is that ethnicity tools are not well understood by consumers in terms of the timeframe that is being revealed, and it’s not consistent between vendors, nor are the results. In some cases, they are flat out wrong, as with Ancestry, and can be proven. This does not engender a great deal of confidence. I only view these results as “interesting” or utilize them in very specific situations and then only using the individual admixture tools at www.Gedmatch.com on individual chromosome segments.

As Judy Russell says, “it’s not soup yet.” That doesn’t mean it’s not interesting though, so long as you understand the difference between interesting and gospel.

With the explosion of genetic genealogy testing, as one might expect, the demand for education, and in particular, basic education has exploded as well.

I’ve written a 101 series, Kelly Wheaton wrote a series of lessons and CeCe Moore did as well. Recently Family Tree DNA has also sponsored a series of free Webinars. I know that at least one book is in process and very near publication, hopefully right after the first of the year. We saw several conferences this year that provided a focus on Genetic Genealogy and I know several are planned for 2014. Genetic genealogy is going mainstream!!! Let’s hope that 2014 is equally as successful and that all these folks asking for training and education become avid genetic genealogists.

I want to close by taking a minute to thank the thousands of volunteers who make such a difference. All of the project administrators at Family Tree DNA are volunteers, and according to their website, there are 7829 projects, all of which have at least one administrator, and many have multiple administrators. In addition, everyone who answers questions on a list or board or on Facebook is a volunteer. Many donate their time to coordinate events, groups, or moderate online facilities. Many speak at events or for groups. Many more write articles for publications from blogs to family newsletters. Additionally, there are countless websites today that include DNA results…all created and run by volunteers, not the least of which is the ISOGG site with the invaluable ISOGG wiki. Without our volunteer army, there would be no genetic genealogy community. Thank you, one and all.

2013 has been a banner year, and 2014 holds a great deal of promise, even without any surprises. And if there is one thing this industry is well known for….it’s surprises. I can’t wait to see what 2014 has in store for us!!! All I can say is hold on tight….

Recently, a Neanderthal toe bone yielded enough DNA to sequence the full genome of the woman whose remains were found in the Denisova Cave in the Altai Mountains, shown above. This information was published in the Journal Nature in an article titled “The complete genome sequence of a Neanderthal from the Altai Mountains” by Prufer et al. I wrote about what was found here, but it wasn’t until I really read the 200+ pages of supplemental information that I found additional buried information.

The article itself talks about some of the findings relative to Native Americans, but the supplemental information provides additional detail and the supporting charts.

In the paper, the Mixe and the Karitiana people of Mexico and Brazil, respectively were most often used to represent Native Americans. There are about 90,000 Mixe language speakers alive today, so their population is not small. However, the Karitiana are just the opposite, with only about 320 people in a very remote region of Brazil. The Karitiana shun contact with outsiders. In some parts of this study, additional population groups were used for additional Native samples.

Here’s what the article itself has to say about Neanderthals, Denisovans and Native Americans.

Denisovan gene flow in mainland Asia

We used the two high-coverage archaic genomes and a hidden Markov model (HMM) to identify regions of specifically Neanderthal and specifically Denisovan ancestry in 13 experimentally phased present-day human genomes (Supplementary Information sections 4 and 13). In the Sardinian and French genomes from Europe we find genomic regions of Neanderthal origin and few or no regions of Denisovan origin. In contrast, in the Han Chinese, the Dai in southern China, and the Karitiana and Mixe in the Americas, we find, in addition to regions of Neanderthal origin, regions that are consistent with being of Denisovan origin (Zscore54.3 excess relative to the Europeans) (Supplementary Information section 13), in agreement with previous analysis based on low-coverage archaic genomes. These regions are also more closely related to the Denisova genome than the few regions identified in Europeans (Supplementary Information section 13). We estimate that the Denisovan contribution to mainland Asian and Native American populations is ,0.2% and thus about 25 times smaller than the Denisovan contribution to populations in Papua New Guinea and Australia. The failure to detect any larger Denisovan contribution in the genome of a 40,000-year-old modern human from the Beijing area suggests that any Denisovan contribution to modern humans in mainland Asia was always quantitatively small. In fact, we cannot, at the moment, exclude that the Denisovan contribution to people across mainland Asia is owing to gene flow from ancestors of present-day people in Oceania after they mixed with Denisovans. We also note that in addition to this Denisovan contribution, the genomes of the populations in Asia and America appear to contain more regions of Neanderthal origin than populations in Europe (Supplementary Information sections 13 and 14).

The fascinating part of this, aside from the fact that Native people also carry both Denisovan and Neanderthal DNA, and that they carry more than Europeans, is that the Denisovan and Neanderthal DNA that they carry is different than that carried by Europeans. In fact, it appears that not all Europeans carry Denisovan DNA and this paper lowers the estimated percentage of Neanderthal for all Europeans.

This difference in the Neanderthal and Denisovan DNA might be able to help solve a long-standing mystery, and that’s whether or not part of the Native population of the Eastern seaboard, and in particular, the far Northeast part of that region, was populated by or admixed with Europeans long before the time of Columbus and other European pre-colonial explorers. This information, of course would have to come from pre-contact burials, but they do exist and with this new information in hand, they might just yield answers never before available.

Dr. Ricki Lewis, in her DNA Science Blog, mentioned something else quite interesting culled from a Christmas Day issue of Nature titled “Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico.” In a nutshell, from article introduction, we find this commentary:

“The risk haplotype carries four amino acid substitutions, all in SLC16A11; it is present at ~50% frequency in Native American samples and ~10% in east Asian, but is rare in European and African samples. Analysis of an archaic genome sequence indicated that the risk haplotype introgressed into modern humans via admixture with Neanderthals.”

Ricki extrapolated on this further:

“Researchers determine the degree to which a mutant gene differs from the most common sequence (wild type), then impose a time scale in the form of known mutation rates. The SLC16A11 five-site haplotype is so divergent that it goes back to nearly 800,000 years ago — before our ancestors expanded out of Africa.

The most plausible explanation, unexpected I suspect, seemed to be that the haplotype came from an archaic human – a Neanderthal or Denisovan or their as-yet unnamed contemporaries. And the haplotype indeed shows up in the skeleton of a Neanderthal found in the Denisovan cave in Siberia.”

And so, it seems that the Native American people today indeed inherited their propensity for type 2 diabetes from their ancient Neanderthal ancestors who lived in the Altai Mountains. It also appears that this genetic predisposition did not carry forward to Europe, if indeed this group of Neanderthals was ancestral to Europeans at all.

Like this:

My family tree, it seems, is quite a mess,
John’s Y DNA did not match Mackness,
John instead matches up to an Ibling,
But then the Ibling did not match his sibling,
Instead the Ibling matched up to a Rolland,
But Rolland wasn’t from here, but from Poland.
The only thing in common I can remember
Is that all of them were born in September.

Good Heavens, I might have figured this out,
There’s one magical man, roly-poly and stout,
That visits worldwide just once a year,
In just one night, bringing gifts and good cheer.
Cookies and milk are left for his snack,
With a wink, he finds gifts for good kids in his pack,
But maybe he had something extra special in stow
For a few grateful Moms under the mistletoe?
My gosh, I think there’s even a song,
About kids seeing Santa kissing on Mom.
All this time, I thought sure it was Dad,
And Dad surely is going to be mad.

Do you think it’s possible that all these odd matches at play
Could be related to the man with the reindeer and the sleigh?
He’s been around forever it seems,
But not in even my wildest dreams,
Does it seem possible that the man with the twinkle and jingle,
Would be the guy doing the Mistletoe Mingle?
However, the modus operandi really does fit
And all I need now is some Santa Claus spit,
Cause, of course, I’m just dying to know,
If John, Ibling and Rolland all line up in a row.
And the name they all match, of course, would be Kringle,
Which would explain all about that wink, twinkle and jingle….

Share this:

Like this:

There is nothing I love more than a happy ending. Second to that perhaps is to know that my blog or work helped someone, and in particularly, helped someone document their Native heritage. In doing so, this confirms and unveils one more of our elusive Native people in early records.

I recently received a lovely thank you note from Shawn Potter. We had exchanged notes earlier, after I wrote “The Autosomal Me” series, about how to utilize small segments of Native American (and Asian) DNA to identify Native American lines and/or ancestors. This technique is called Minority Admixture Mapping (MAP) and was set forth in detail in various articles in the series.

Shawn’s note said: “I’ve been doing more work on this segment and others following your method since we exchanged notes. I’m pretty sure I’ve found the source of this Native American DNA — an ancestor named John Red Bank Payne who lived in North Georgia in the late 18th and 19th centuries. Many of his descendants believe on the basis of circumstantial evidence that his mother was Cherokee. I’ve found 10 descendants from four separate lines that inherited matching Native American DNA, pointing to one of his parents as the source.”

Along with this note, Shawn attached a beautiful 65 page book he had written for his family members which did document the Native DNA, but in the context of his family history. He included their family story, the tales, the genealogical research, the DNA evidence and finally, a chapter of relevant Cherokee history complete with maps of the area where his ancestors lived. It’s a beautiful example of how to present something like this for non-DNA people to understand. In addition, it’s also a wonderful roadmap, a “how to” book for how to approach this subject from a DNA/historical/genealogical perspective. As hard as it is for me to sometimes remember, DNA is just a tool to utilize in the bigger genealogy picture.

Shawn has been gracious enough to allow me to reprint some of his work here, so from this point on, I’ll be extracting from his document. Furthermore, Elizabeth Shown Mills would be ecstatic, because Shawn has fully documented and sourced his document. I am not including that information here, but I’m sure he would gladly share the document itself with any interested parties. You can contact Shawn at shpxlcp@comcast.net.

From the book, “Cherokee Mother of John Red Bank Payne” by Shawn Potter and Lois Carol Potter:

Descendants of John Red Bank Payne describe his mother as Cherokee. Yet, until now, some have questioned the truth of this claim because genealogists have been unable to identify John’s mother in contemporary records. A recent discovery, however, reveals both John Red Bank Payne and his sister Nancy Payne inherited Native American DNA.

Considering information from contemporary records, clues from local tradition, John’s name itself, and now the revelation that John and his sister inherited Native American DNA, there seems to be sufficient evidence to say John Red Bank Payne’s mother truly was Cherokee. The following summary describes what we know about John, his family, and his Native American DNA.

John Red Bank Payne was born perhaps near present-day Canton, Cherokee County, Georgia, on January 24, 1754, married Ann Henslee in Caswell County, North Carolina, on March 5, 1779, and died in Carnesville, Franklin County, Georgia, on December 14, 1831.

John’s father, Thomas Payne, was born in Westmorland County, Virginia, about 1725, and owned property in Halifax and Pittsylvania counties, Virginia, as well as Wilkes County, North Carolina, and Franklin County, Georgia. Several factors suggest Thomas travelled with his older brother, William, to North Georgia and beyond, engaging in the deerskin trade with the Cherokee Nation during the mid 1700s. Thomas Payne died probably in Franklin County, Georgia, after February 23, 1811.

Contemporary records reveal Thomas had four children (William, John, Nancy, and Abigail) by his first wife, and nine children (Thomas, Nathaniel, Moses, Champness, Shrewsbury, Zebediah, Poindexter, Ruth, and Cleveland) by his second wife Yanaka Ayers. Thomas married Yanaka probably in Halifax County, Virginia, before September 20, 1760.

Local North Georgia tradition identifies the first wife of Thomas Payne as a Cherokee woman. Anna Belle Little Tabor, in History of Franklin County, Georgia, wrote that “Trader Payne” managed a trading post on Payne’s Creek, and “one of his descendants, an offspring of his Cherokee marriage, later married Moses Ayers whose descendants still live in the county.”

Descendants of John Red Bank Payne also cite his name Red Bank, recorded in his son’s family Bible, as evidence of his Cherokee heritage. Before the American Revolution, British Americans rarely defied English legal prohibitions against giving a child more than one Christian name. So, the very existence of John’s name Red Bank suggests non-English ethnicity. On the other hand, many people of mixed English-Cherokee heritage were known by their Cherokee name as well as their English first and last names during this period.

Furthermore, while the form of John’s middle name is unlike normal English names, Red Bank conforms perfectly to standard Cherokee names. It also is interesting to note, Red Bank was the name of a Cherokee village located on the south side of Etowah River to the southwest of present-day Canton, Cherokee County, Georgia.

While some believe the above information from contemporary records and clues from local tradition, as well as John’s name Red Bank, constitute sufficient proof of John’s Cherokee heritage, recently discovered DNA evidence confirms at least one of John’s parents had Native American ancestry. Ten descendants of John Red Bank Payne and his sister Nancy Payne, representing four separate lineages, inherited six segments of Native American DNA on chromosomes 2, 3, 5, 8, 13, and 18 (see Figure 1 for the relationship between these descendants; Figures 2-7 for images of their shared Native American DNA; and https://dna-explained.com/2013/06/02/the-autosomal-me-summary-and-pdf-file/ for an explanation of this method of identifying Native American chromosomal segments).

In this segment, Bert P, Rosa P, Nataan S, Cynthia S, and Kendall S inherited matching Native American DNA described as Amerindian, Siberian, Southeast Asian, and Oceanian by the Eurogenes V2 K15 admixture tool, and as North Amerind, Mesoamerican, South America Amerind, Arctic Amerind, East Siberian, Paleo Siberian, Samoedic, and East South Asian by the Magnus Ducatus Lituaniae Project World22 admixture tool. Since their common ancestors were Thomas Payne and his wife, the source of this Native American DNA must be either Thomas Payne or his wife. See Figures 2a-2g.

Note: Since Native Americans and East Asians share common ancestors in the pre-historic past, their DNA is similar to each other in many respects. This similarity often causes admixture tools to interpret Native American DNA as various types of East Asian DNA. Therefore, the presence of multiple types of East Asian DNA together with Native American DNA tends to validate the presence of Native American DNA.

Roberta’s Summary: Shawn continues to document the other chromosome matches in the same manner. In total, he has 10 descendants of Thomas Payne and his wife, who it turns out, indeed was Cherokee, as proven by this exercise in combination with historical records. These people descend through 2 different children. Cynthia and Kendall descend through daughter Nancy Payne, and the rest of the descendants descend through different children of John Red Bank Payne. All of the DNA segments that Shawn utilized in his report share Native/Asian segments in both of these family groups, the descendants of both Nancy and John Red Bank Payne.

Shawn’s success in this project hinged on two things. First, being able to test multiple (in this case, two) descendants of the original couple. Second, he tested several people and had the tenacity to pursue the existence of Native DNA segments utilizing the Minority Admixture Mapping (MAP) technique set forth in “The Autosomal Me” series. It certainly paid off. Shawn confirmed that the wife of Thomas Payne was, indeed Native, most likely Cherokee since he was a Cherokee trader, and that today’s descendants do indeed carry her heritage in their DNA.

Great job Shawn!! Wouldn’t you love to be his family member and one of the recipients of these lovely books about your ancestor! Someone’s going to have a wonderful Christmas!

This week, in the journal Nature, scientists reported on the full sequencing of a Neanderthal toe bone found in the Denisova Cave in the Altai Mountains, the location where the Denisovan skeleton found in 2008 and sequenced earlier this year was also found.

We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.

The abstract also includes this graphic from the paper

This sequence is significant because of a number of unique findings.

The skeleton showed physical traits of both Neanderthals and modern humans and is thought to be about 50,000 years old.

Genetic sequencing revealed that this bone belonged to a Neanderthal woman, not a Denisovan, although other Denisovan remains, including one previously sequenced, have been found in this cave.

The closest genetic relative is found in the Mezmaiskaya Cave in the Caucasus Mountains, some 2000+ miles distant. Admittedly, we don’t have a lot of sequenced remains for comparison.

Sequencing revealed a heretofore unknown genetic line of archaic humans. This person obtained from between 2.7 to 5.8 percent of their genome from this unknown line. That percentage is equal to someplace between a great-great-great-grandparent and a great-great-great-great-great-grandparent, assuming only one ancestor was involved. If this unknown human lineage was admixed into the population in multiple individuals, then the trace amounts could be passed around forever, just like the Neanderthal and Denisovan lineages are in Europeans today.

This unknown line could be homo erectus.

There is no evidence that this unknown human lineage interbred with either modern humans or Neanderthals. I would presume this means that this unknown line then bred with the Denisovan group which did not manifest itself in contemporary humans.

This individual was inbred with their parents being closely related, possibly half-siblings or an uncle and niece, or an aunt and nephew or a grandfather and granddaughter or grandmother and grandson. Inbreeding was also common among the woman’s recent ancestors. Another article headline this week pronounced that “Neanderthals Liked Incest” which I found to be offensive. Incest is a highly negatively charged cultural word. In the not so recent past, the practice of inbreeding was perfectly acceptable in European royalty. Furthermore, we have no idea how these people felt about inbreeding, hence the word “liked” is misleading. It could well be that they lived in a small nuclear family group and there were no other choices for partners. There could also be other cultural and selection factors at play here of which we are unaware. For example, perhaps males were more protective of mothers and children to whom they were related than ones where they had no family or group ties – increasing the likelihood of survival of offspring of women to whom the males were related.

At least half of a percent of the Denisovan genome came from Neanderthals, but none of the Denisovan genome has yet been detected in Neanderthals. If this holds, it would imply that our ancestors either bred with Neanderthals and Denisovans separately, or with Denisovans who carried Neanderthal DNA. Given that most Europeans carry more Neanderthal DNA than Denisovan, the second scenario alone is unlikely. It’s also possible that we simply haven’t found Neanderthal’s who did carry Denisovan DNA.

More than 31,000 differences were found between modern humans and Neanderthals and Denisovans, many having to do with brain development.

Dienekes discussed this research in his blog as well. Note his “family tree.”